From d18af35796f370acae1de2ff0240ec84895c2464 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Mon, 28 Mar 2022 15:28:51 +0000
Subject: [PATCH] update tuto
---
src/tutorial_htrsim.Rmd | 58 ++++++++++++++++++++++++++++++++++-------
1 file changed, 49 insertions(+), 9 deletions(-)
diff --git a/src/tutorial_htrsim.Rmd b/src/tutorial_htrsim.Rmd
index 36d2092..40526a2 100644
--- a/src/tutorial_htrsim.Rmd
+++ b/src/tutorial_htrsim.Rmd
@@ -9,21 +9,15 @@ $$
Phenotype = Genotype + Environment + Genotype.Environment
$$
From this expression, $\beta_{G}$, $\beta_{E}$, $\beta_{G*E}$ can be seen as coefficients which allow quantifying the participation of each factors (Genotype, Environment and interaction Genotype/Environment).
-Then,
+In mathematical term, it leads to a linear expression such:
$$
P = \beta_{G}*G + \beta_{E}*E + \beta_{G*E}*G.E + \beta_{0}
$$
In order to estimate these coefficients, a Generalized Linear Model (GLM) can be used.
+# B. HTRSIM getting started
-```{r echo=FALSE, out.width='100%'}
-knitr::include_graphics('../img/schema_loop.jpg')
-```
-
-
-
-This is a tutorial for *htrsim* utilization
-
+ <u>a. Required</u>
```{r required, message=FALSE, echo = T, results = "hide"}
library(data.table)
@@ -40,6 +34,52 @@ setwd("/home/rstudio/mydatalocal/counts_simulation/src/")
```
+ <u>b. Workflow</u>
+
+
+```{r echo=FALSE, out.width='50%'}
+knitr::include_graphics('../img/schema_loop.jpg')
+```
+
+ <u>c. RNA-seq pipeline</u>
+
+You can used your favorite pipeline to obtain table counts from real data.
+If you don't have any idea of how to obtain such table counts rdv [at](https://gitbio.ens-lyon.fr/aduvermy/rna-seq_public_library_investigations)
+
+
+ <u> d. BioProject PRJNA675209b as input</u>
+
+To easily test *HTRSIM* we produced an usual table counts from BioProject PRJNA675209b.
+Take the time to clean up your table counts.
+
+```{r}
+tabl_cnts <- read.table("/home/rstudio/mydatalocal/rna-seq_public_library_investigations/results/2022-02-09/salmon.merged.gene_counts.tsv", header = TRUE)
+rownames(tabl_cnts) <- tabl_cnts$gene_id
+tabl_cnts <- tabl_cnts %>% select(-gene_id)##suppr colonne GeneID
+tabl_cnts <- tabl_cnts %>% select(-gene_name) ##suppr colonne GeneName
+tabl_cnts
+```
+
+ <u> e. Launch HTRSIM</u>
+
+```{r message=FALSE, warning=FALSE}
+## import design of bioProject
+bioDesign <- read_csv2(file = "/home/rstudio/mydatalocal/rna-seq_public_library_investigations/data/design_deseq__PRJNA675209.csv")
+#bioDesign
+source(file = "htrsim/main.R")
+tabl_cnts %>% dim()
+bioDesign %>% dim()
+simul_cnts = htrsim(tabl_cnts, bioDesign = bioDesign, 2)
+```
+
+
+
+
+# C. Advance user
+
+
+This is a tutorial for *htrsim* utilization
+
To perform counts per genes *htrsim* needs some inputs.</br>
Following parameters are required:</br>
- number of samples</br>
--
GitLab